label add text to bdf label record

scale scale factors

uov overall isotropic thermal displacement parameter U

extinc extinction factors

prolod special quantities to be stored inlogical record atom

scale1¹PDB orthogonal to fractional coordinate transformation

scale2¹PDB orthogonal to fractional coordinate transformation

scale3^1,2PDB orthogonal to fractional coordinate transformation

shift coordinate shift or inversion through centre of symmetry

symop transform all fractional coordinates by this operator

defaul set any unsupplied parameters to these default values

atom PDB atom parameters

proat free format version of the PDB ATOM line

proati free format version of the PDB ATOM line

proatd free format version of the PDB ATOM line

proate free format version of the PDB ATOM line

hetatm PDB heteroatom parameters

prohet free format version of PDB HETATM line

sigatm³PDB standard deviation of atom paramter

prosga³ free format version of PDB SIGATM line

anisou³ PDB anisotropic temperature factor line

proani³free format version of PDB ANISOU line

siguij³ PDB standard deviation of anisotropic temperature factor

prosgu³ free format version of PDB SIGUIJ line

1 Indicates that all three lines must be given for a bdf which is not the output of PROATM; after that these lines are optional.

2 The scale3 line marks the end of the preliminary, general data input lines. From shift to prosgu the order of input lines is somewhat flexible.

3 Indicates that the line must follow the atom parameter line to which it applies.

The designation of atom name in any but the atom, proato, hetatm or prohet lines is ignored. The auxiliary lines will be loaded as if part of the preceeding atom parameter line.

All checking is done against the PDB serial number given in the first field of the atom parameter lines atom, proat, hetatm or prohet.

PROATM Option Code

thermal parameter¹ over overall isotropic U

uis indiv. isotropic U in PDB

bis indiv. isotropic B in PDB

aniso indiv. anisotropic in PDB

mixed mixed iso and aniso

print atoms on bdf print yes

nopr no

punch PDB data npc no

pch yes

input bdf atoms merge merge previous atoms

apriori delete previous atoms

output bdf atoms lod load atoms to output bdf

nol only print or punch atom list

data set number dsn n 1

distinguish B & U² bcut t U's < t < B's 0.633

1The specifications ova, iso, aniso and mixed specify the form the thermal displacement parameters will be stored in the output bdf.

2 The value t is the threshold of U values entered on atom and hetatm lines. The default is set at 0.633 which is B=50.0

scale 1 scale factor

2 scale group 1

3 dataset name parent

uov 1 overall isotropic displacement parameter U

2 data set name parent

extinc 1 extinction correction method

zach Zachariasen

typ1 Becker-Coppens, type I

typ2 Becker-Coppens, type II

gen Becker-Coppens, type I and II

2 temperature factor type

is isotropic

an anisotropic (not implemented)

3 mosaic distribution

gaus Gaussian distribution

lore Lorentzian distribution

4 isotropic extinction parameter (g for zach or typ1) 0

5 isotropic extinction parameter (ρ for typ2 or gen) 0

6 mean value of T 0.3 Xray 1.5 neutron

prolod 1- mnemonics of atom parameters to be loaded into the bdf

The character and integer mnemonics are listed in the Reference Manual in the section on quantities stored in logical record atom

The fields of the prolod line describe the quantities which are to be placed in logical record atom of the bdf. If the prolod line is omitted, the quantities stored depend upon the temperature factor type selected.

ova x, y, z, sft, res, seq, rsq, sqn, foo

iso the above plus u

aniso the above plus u, u11, u22, u33, u12, u13, u23

mixed the same as aniso plus tft

All X, Y, Z parameters are stored in the bdf as fractional coordinates; all isotropic temperature factors are stored as U; all anisotropics as Uij. For printing and punching appropriate conversions are made to the PDB conventions.

scalej(where j is 1, 2 and 3)

1 S(j, 1) orthog.-to-fract. transformation matrix element

2 S(j, 2) " " "

3 S(j, 3) " " "

4 U(j) vector

shift 1-3 translational shift of fractional coordinates x, y, z 0

symop 1-9 rotation elements ,, ,,......

10-12 translation elements ,,

defaul 1- default values in order for the loadp line

atom(standard groups) and hetatm(non-standard groups)

1 atom serial number

2 atom type symbol

3 alternate location indicator

4 residue name

5 chain identifier

6 residue sequence number

7 code for insertion of residues

8-10 x, y, z in orthogonal Å

11 population (occupancy) parameter

12 temperature factor U

13 footnote number

proatand prohet

1 atom serial number or code (max 10000)

n mean next integer since last atom

2 scattering factor type as chemical symbol in upper case¹

3 remoteness indicator code¹

Aa Bb Gg Dd Ee Zz Hh

4 branch designator integers 0-9

5 alternate location indicator letters A, B,....

6 three- or four-letter residue name (e.g. ARG, PRO,...)

7 chain identifier - three char max (e.g. A for hemoglobin α)

8 residue sequence number (max 10000)

9 code for insertion of residues (e.g. A, B,...)

10-12 x, y, z coordinates in orthogonal Å

13 population parameter (occupancy) 1

14 temperature factor U² 0.12665

15 footnote number 0

16 anomalous population parameter 1

1 The chemical symbol may be the number n followed by H, where n is 1-3 for a sub-branch indicator of hydrogen atoms.

2 Note the U threshold on the PROATM line.

proatd 1 first serial number of atom to be deleted from the bdf

2 last serial number of atom to be deleted from the bdf

proati(used with proate line)

1 serial number of the atom preceding the insertion

proate(used with proati line)

1 serial number of the last atom that may resequenced as a result of the insertion and renumbering last atom number

prosig1 serial number

2-4 σx, σy, σz (in orthogonal Å)

5 σPP

6 σU

7 σAPP

prouij 1 serial number

2-7 ,,,, , (x10⁴)

prosgu1 serial number

2-7 σ, σ, ..... σ (x10⁴)

sigatm 1-7 atom id. as in atom line

8-10 σx, σy, σz in orthogonal Å

11 σPP

12 σU

13 σAPP

anisou1-7 atom id. as in atom line

8-13 ,,,, , (x10⁴)

siguij1-7 atom id. as in atom line

8-13 σ, σ, ...... σ (x10⁴)